chr5-170267053-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005565.5(LCP2):āc.644A>Gā(p.Asn215Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000285 in 1,613,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005565.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCP2 | NM_005565.5 | c.644A>G | p.Asn215Ser | missense_variant | 9/21 | ENST00000046794.10 | |
LCP2 | XM_047417171.1 | c.413A>G | p.Asn138Ser | missense_variant | 7/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCP2 | ENST00000046794.10 | c.644A>G | p.Asn215Ser | missense_variant | 9/21 | 1 | NM_005565.5 | P1 | |
LCP2 | ENST00000521416.5 | c.29A>G | p.Asn10Ser | missense_variant | 1/13 | 2 | |||
LCP2 | ENST00000520344.1 | c.29A>G | p.Asn10Ser | missense_variant | 1/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 249272Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135230
GnomAD4 exome AF: 0.000285 AC: 416AN: 1461684Hom.: 0 Cov.: 31 AF XY: 0.000249 AC XY: 181AN XY: 727120
GnomAD4 genome AF: 0.000289 AC: 44AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.644A>G (p.N215S) alteration is located in exon 9 (coding exon 9) of the LCP2 gene. This alteration results from a A to G substitution at nucleotide position 644, causing the asparagine (N) at amino acid position 215 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at